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Scandal elevated Kerry Gilpin to the head of the Massachusetts State Police, and her two-year tenure never escaped its shadow.

Gilpin said Wednesday that she will step down after presiding over a succession of crises — most notably a sprawling overtime fraud scheme — that exposed systemic problems and badly eroded public trust. Her departure may be the first of many changes at the state’s largest law enforcement agency, with Governor Charlie Baker weighing a new package of reforms.

In a letter to the department, Gilpin described her time as colonel as “the greatest honor of my professional life” while acknowledging that it had “presented tremendous challenges.”

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“It remains deeply disheartening to me that a small number of our personnel chose to violate our principles and values,” Gilpin wrote. “We have taken action to address their transgressions, conducting thorough and painstaking internal investigations as well as criminal investigations. I have been tremendously disappointed that some members of this remarkable organization have betrayed the public trust that so many of us worked so hard to earn.”

Gilpin, 49, has come under sharp criticism for maintaining a studiously low profile during the swirling controversies, and on Wednesday was not made available to answer questions about her departure. But those familiar with her work said that she did her best to put the agency on the right path.

“She really worked hard; her heart was in the right place,” said former Boston police commissioner Kathleen O’Toole, who worked with Gilpin as an unpaid consultant to help overhaul the department.

O’Toole, who oversaw the state law enforcement agency in the 1990s, said Gilpin navigated “the most challenging period in State Police history” with “authenticity, integrity, and humility.”

“What the department needed most was somebody with integrity, and Kerry Gilpin has integrity,” she said. “No one has ever questioned that.”

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Gilpin will retire Nov. 15, the same date she took over two years ago, according to State Police spokesman David Procopio.

Governor Charlie Baker said Gilpin felt she had accomplished what she wanted to in the job and “simply wanted to move on to do other things.” He dismissed the suggestion that internal politics played a role in her departure.

“The decision obviously was hers,” Baker told reporters at the State House. “I can’t make decisions for people like that. The biggest challenges that she faced, in my view, coming right through the front door were dealing with probably one of the most significant scandals in the department’s history. And I’m sure anybody pursuing an agenda like that inside an organization like that would be wary.”

Baker declined to discuss whom he might name as a replacement, saying he would make an announcement in the coming days. Her successor will face a considerable challenge, he said.

“There’s a lot of work that remains to be done there to restore the reputation of that organization,” he said.

Baker said he is planning to file a legislative package that will include proposals to overhaul the agency. The details are unclear, but Baker has said he is open to allowing candidates from outside the State Police to be considered for its top position, which would require a change in state law.

“I think you can expect to see that in there,” he said.

Gilpin makes $241,845 a year. She could be in line for a pension of roughly $180,000, under a formula that allows State Police personnel with at least 25 years of service to retire with 75 percent of their most recent salary.

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In her letter, Gilpin said she was “fully committed to restoring that trust to ensure that the actions of a few do not overshadow the reputation and hard work of the vast majority who conduct themselves with the utmost integrity every day.”

“We have accomplished so much during this difficult time,” Gilpin added. “And I am confident that you will continue to build upon this foundation.”

The State Police Association, a union that represents most department personnel, said Gilpin’s tenure had “ushered in a new era of modernization and reform.”

She disbanded Troop E, the division at the center of the overtime abuse scandal, had GPS tracking installed in cruisers to make sure troopers worked their shifts, and launched a pilot body camera program.

Yet she also managed a department battered by controversy, from claims of widespread fraud and systemic corruption to individual troopers charged for various crimes.

Recruitment and promotion practices came under fire after complaints of discrimination. Department officials hid, destroyed, and lost track of records that could have exposed wrongdoing. The department’s head of payroll pleaded guilty to embezzling thousands of dollars. Two weeks ago, a trooper was charged after a couple accused him of inappropriately touching himself and punching one of them in the face at a Luke Bryan concert at Gillette Stadium in June.

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The payroll scandal implicated 46 troopers, including 10 who were charged criminally. An internal probe, which was initiated months before Gilpin became colonel but officials say she expanded, flagged the troopers, and Gilpin referred the case to prosecutors.

Years before the fraud became public, department leaders, including Gilpin, encountered a host of warning signs, but there is little evidence they acted to address them.

Gilpin joined the State Police in 1994, having turned to a career in law enforcement after the 1986 murder of her sister, Tracy, whose killing went unsolved until an arrest was made four months after Gilpin became colonel.

A sergeant in 2013, she was promoted several times in subsequent years. In her last role, she was a deputy division commander overseeing internal affairs and the State Police training academy.

Her ascension to the top of the 2,200-member force was unexpected, even by her.

In late 2017, e-mails indicate, Gilpin was on vacation in the Dominican Republic when news broke that then-colonel Richard McKeon and other top commanders had ordered troopers to scrub embarrassing information from an arrest report about a judge’s daughter. McKeon resigned and Gilpin was sworn in as colonel the following week.

Dennis Galvin, president of the Massachusetts Association for Professional Law Enforcement and a retired State Police major, said Gilpin was “put in an unenviable position” from the start. Throughout her tenure, it appeared Gilpin’s hands were tied by her supervisors in the Executive Office of Public Safety and Security, the governor’s office, or both, he said.

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“She did what she could do,” Galvin said. “But she was not given the proper support from the governor and everybody else to really tackle the issues that are affecting the department.”


Travis Andersen of the Globe staff contributed to this report. Matt Rocheleau can be reached at matthew.rocheleau@globe.com. Follow him on Twitter @mrochele. Matt Stout can be reached at matt.stout@globe.com. Follow him on twitter @mattpstout. Andrea Estes can be reached at estes@globe.com.